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Genome-wide association mapping of root traits in a japonica rice panel.

Courtois B, Audebert A, Dardou A, Roques S, Ghneim-Herrera T, Droc G, Frouin J, Rouan L, Gozé E, Kilian A, Ahmadi N, Dingkuhn M - PLoS ONE (2013)

Bottom Line: Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04.The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion.Several likely candidate genes were found in close proximity to these loci.

View Article: PubMed Central - PubMed

Affiliation: Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Montpellier, France.

ABSTRACT
Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r(2)>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates.

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Related in: MedlinePlus

Distribution of selected traits.SB =shoot biomass; NBT = Tiller number; DRB = deep root biomass; NBR_30 = number of roots below 30 cm; R_S = root/shoot mass ratio; LENGTH = maximum root length .
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pone-0078037-g003: Distribution of selected traits.SB =shoot biomass; NBT = Tiller number; DRB = deep root biomass; NBR_30 = number of roots below 30 cm; R_S = root/shoot mass ratio; LENGTH = maximum root length .

Mentions: Moderate to large variation was observed for most root parameters, with CVs varying from 13% for DEPTH to 103% for RBB30 (Table 3). The distribution of the root parameters were globally normal, with the exceptions of NBR_30, RB2030 and RBB30, which had skewed distributions due to the presence of accessions with shallow roots that did not exceed 30 cm in length (Figure 3). The broad-sense heritabilities based on genotypic means, which measure the reproducibility of the experiment, were also reasonably high, varying from 0.66 for NBR_30 to 0.89 for DRP. The six subpopulations of the panel differed in terms of means for all traits except for RB0020 (Table 4). Subpopulations 1 (upland rice varieties from Africa and Latin America), 2 (traditional upland varieties of equatorial Asia) and 3 (upland rice varieties from Southeast Asia) were showing the deepest roots (high NBR_30, DRB, DRP, DEPTH and LENGTH) with subpopulation 3 characterized by a larger biomass (NBT, SB, RB and PB) than subpopulations 1 and 2. Subpopulations 4 (temperate accessions) and 5 (bulu types) were showing a large shoot biomass, similar root mass in the shallow horizon than the other subpopulations but much more limited root mass in depth and low R_S. Sub-population 6 (accessions derived from Colombia 1) was composed of small size accessions with limited shoot biomass (low LLGTH, NBT, SB and PB), limited root development and intermediate R_S. The admixed group was intermediate for most traits.


Genome-wide association mapping of root traits in a japonica rice panel.

Courtois B, Audebert A, Dardou A, Roques S, Ghneim-Herrera T, Droc G, Frouin J, Rouan L, Gozé E, Kilian A, Ahmadi N, Dingkuhn M - PLoS ONE (2013)

Distribution of selected traits.SB =shoot biomass; NBT = Tiller number; DRB = deep root biomass; NBR_30 = number of roots below 30 cm; R_S = root/shoot mass ratio; LENGTH = maximum root length .
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3818351&req=5

pone-0078037-g003: Distribution of selected traits.SB =shoot biomass; NBT = Tiller number; DRB = deep root biomass; NBR_30 = number of roots below 30 cm; R_S = root/shoot mass ratio; LENGTH = maximum root length .
Mentions: Moderate to large variation was observed for most root parameters, with CVs varying from 13% for DEPTH to 103% for RBB30 (Table 3). The distribution of the root parameters were globally normal, with the exceptions of NBR_30, RB2030 and RBB30, which had skewed distributions due to the presence of accessions with shallow roots that did not exceed 30 cm in length (Figure 3). The broad-sense heritabilities based on genotypic means, which measure the reproducibility of the experiment, were also reasonably high, varying from 0.66 for NBR_30 to 0.89 for DRP. The six subpopulations of the panel differed in terms of means for all traits except for RB0020 (Table 4). Subpopulations 1 (upland rice varieties from Africa and Latin America), 2 (traditional upland varieties of equatorial Asia) and 3 (upland rice varieties from Southeast Asia) were showing the deepest roots (high NBR_30, DRB, DRP, DEPTH and LENGTH) with subpopulation 3 characterized by a larger biomass (NBT, SB, RB and PB) than subpopulations 1 and 2. Subpopulations 4 (temperate accessions) and 5 (bulu types) were showing a large shoot biomass, similar root mass in the shallow horizon than the other subpopulations but much more limited root mass in depth and low R_S. Sub-population 6 (accessions derived from Colombia 1) was composed of small size accessions with limited shoot biomass (low LLGTH, NBT, SB and PB), limited root development and intermediate R_S. The admixed group was intermediate for most traits.

Bottom Line: Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04.The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion.Several likely candidate genes were found in close proximity to these loci.

View Article: PubMed Central - PubMed

Affiliation: Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Montpellier, France.

ABSTRACT
Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r(2)>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates.

Show MeSH
Related in: MedlinePlus